- Author:
- Weiwei Ai <wai484@aucklanduni.ac.nz>
- Date:
- 2024-05-08 11:31:07+12:00
- Desc:
- Add sedml and scripts for SGLT1
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/b65/rawfile/4c70c12474d3ae6c1f083145619576bfaf426439/Electrogenic cotransporter/CellMLV2/SGLT1_BG.py
# The content of this file was generated using the Python profile of libCellML 0.5.0.
from enum import Enum
from math import *
__version__ = "0.4.0"
LIBCELLML_VERSION = "0.5.0"
STATE_COUNT = 6
VARIABLE_COUNT = 99
class VariableType(Enum):
VARIABLE_OF_INTEGRATION = 0
STATE = 1
CONSTANT = 2
COMPUTED_CONSTANT = 3
ALGEBRAIC = 4
VOI_INFO = {"name": "t", "units": "second", "component": "params_BG", "type": VariableType.VARIABLE_OF_INTEGRATION}
STATE_INFO = [
{"name": "q_1", "units": "fmol", "component": "SGLT1_BG", "type": VariableType.STATE},
{"name": "q_2", "units": "fmol", "component": "SGLT1_BG", "type": VariableType.STATE},
{"name": "q_3", "units": "fmol", "component": "SGLT1_BG", "type": VariableType.STATE},
{"name": "q_4", "units": "fmol", "component": "SGLT1_BG", "type": VariableType.STATE},
{"name": "q_5", "units": "fmol", "component": "SGLT1_BG", "type": VariableType.STATE},
{"name": "q_6", "units": "fmol", "component": "SGLT1_BG", "type": VariableType.STATE}
]
VARIABLE_INFO = [
{"name": "V0_Vm", "units": "volt", "component": "params_BG", "type": VariableType.ALGEBRAIC},
{"name": "V_E", "units": "volt", "component": "params_BG", "type": VariableType.ALGEBRAIC},
{"name": "q_Nai", "units": "fmol", "component": "params_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "Nai", "units": "mM", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "V_i", "units": "pL", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_Nao", "units": "fmol", "component": "params_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "Nao", "units": "mM", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "V_o", "units": "pL", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_Glci", "units": "fmol", "component": "params_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "Glci", "units": "mM", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_Glco", "units": "fmol", "component": "params_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "Glco", "units": "mM", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "test_volt", "units": "volt", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "R", "units": "J_per_K_mol", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "T", "units": "kelvin", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "F", "units": "C_per_mol", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_Nai", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_Nao", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_Glci", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_Glco", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_1", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_init_1", "units": "fmol", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_2", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_init_2", "units": "fmol", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_3", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_init_3", "units": "fmol", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_4", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_init_4", "units": "fmol", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_5", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_init_5", "units": "fmol", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "K_6", "units": "per_fmol_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "q_init_6", "units": "fmol", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "z_zf1", "units": "dimensionless", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "z_zr1", "units": "dimensionless", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "z_zf6", "units": "dimensionless", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "z_zr6", "units": "dimensionless", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "kappa_r1", "units": "fmol_per_s_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "kappa_r2", "units": "fmol_per_s_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "kappa_r3", "units": "fmol_per_s_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "kappa_r4", "units": "fmol_per_s_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "kappa_r5", "units": "fmol_per_s_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "kappa_r6", "units": "fmol_per_s_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "kappa_r7", "units": "fmol_per_s_1", "component": "params_BG", "type": VariableType.CONSTANT},
{"name": "I_ss", "units": "fA", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_r6", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "Ii", "units": "fA", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "I_zf1", "units": "fA", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "I_zr6", "units": "fA", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "I_zf6", "units": "fA", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "I_zr1", "units": "fA", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "mu_Nai", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "mu_Nao", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "mu_Glci", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "mu_Glco", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.COMPUTED_CONSTANT},
{"name": "mu_1", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_1", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "mu_2", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_2", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "mu_3", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_3", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "mu_4", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_4", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "mu_5", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_5", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "mu_6", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_6", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "V_Vm", "units": "volt", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "mu_zf1", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "V_zf1", "units": "volt", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_zf1", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "mu_zr1", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "V_zr1", "units": "volt", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_zr1", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "mu_zf6", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "V_zf6", "units": "volt", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_zf6", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "mu_zr6", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "V_zr6", "units": "volt", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_zr6", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_r1", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_f_r1", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_r_r1", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_r2", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_f_r2", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_r_r2", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_r3", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_f_r3", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_r_r3", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_r4", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_f_r4", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_r_r4", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_r5", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_f_r5", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_r_r5", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_f_r6", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_r_r6", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "v_r7", "units": "fmol_per_s", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_f_r7", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC},
{"name": "A_r_r7", "units": "J_per_mol", "component": "SGLT1_BG", "type": VariableType.ALGEBRAIC}
]
def lt_func(x, y):
return 1.0 if x < y else 0.0
def create_states_array():
return [nan]*STATE_COUNT
def create_variables_array():
return [nan]*VARIABLE_COUNT
def initialise_variables(states, rates, variables):
variables[3] = 20.0
variables[4] = 8.5e5
variables[6] = 100.0
variables[7] = 8.5e5
variables[9] = 10.0e-3
variables[11] = 1.0e-12
variables[12] = 0.0
variables[13] = 8.31
variables[14] = 293.0
variables[15] = 96485.0
variables[16] = 3.216e-08
variables[17] = 3.216e-08
variables[18] = 4.848e-06
variables[19] = 4.848e-06
variables[20] = 2.235
variables[21] = 16.605778811026234
variables[22] = 10.437
variables[23] = 16.605778811026234
variables[24] = 8.602
variables[25] = 16.605778811026234
variables[26] = 8.602
variables[27] = 16.605778811026234
variables[28] = 28.628
variables[29] = 16.605778811026234
variables[30] = 0.192
variables[31] = 16.605778811026234
variables[32] = 0.3
variables[33] = 0.3
variables[34] = 0.7
variables[35] = 0.7
variables[36] = 47.905
variables[37] = 2.325
variables[38] = 5.812
variables[39] = 92.998
variables[40] = 0.349
variables[41] = 15.661
variables[42] = 0.029
states[0] = variables[21]
states[1] = variables[23]
states[2] = variables[25]
states[3] = variables[27]
states[4] = variables[29]
states[5] = variables[31]
def compute_computed_constants(variables):
variables[2] = variables[3]*variables[4]
variables[5] = variables[6]*variables[7]
variables[8] = variables[9]*variables[4]
variables[10] = variables[11]*variables[7]
variables[50] = variables[13]*variables[14]*log(variables[16]*variables[2])
variables[51] = variables[13]*variables[14]*log(variables[17]*variables[5])
variables[52] = variables[13]*variables[14]*log(variables[18]*variables[8])
variables[53] = variables[13]*variables[14]*log(variables[19]*variables[10])
def compute_rates(voi, states, rates, variables):
variables[54] = variables[13]*variables[14]*log(variables[20]*states[0])
variables[1] = -0.05 if lt_func(voi, 1204.75e-3) else variables[12] if lt_func(voi, 2984.75e-3) else -0.05
variables[0] = variables[1]
variables[66] = variables[0]
variables[68] = variables[66]
variables[67] = variables[32]*variables[15]*variables[68]
variables[80] = 2.0*variables[51]+variables[54]-variables[67]
variables[56] = variables[13]*variables[14]*log(variables[22]*states[1])
variables[71] = variables[66]
variables[70] = variables[33]*variables[15]*variables[71]
variables[81] = variables[56]+variables[70]
variables[79] = variables[36]*(exp(variables[80]/(variables[13]*variables[14]))-exp(variables[81]/(variables[13]*variables[14])))
variables[64] = variables[13]*variables[14]*log(variables[30]*states[5])
variables[74] = variables[66]
variables[73] = variables[34]*variables[15]*variables[74]
variables[94] = variables[64]-variables[73]
variables[77] = variables[66]
variables[76] = variables[35]*variables[15]*variables[77]
variables[95] = variables[54]+variables[76]
variables[44] = variables[41]*(exp(variables[94]/(variables[13]*variables[14]))-exp(variables[95]/(variables[13]*variables[14])))
variables[55] = -variables[79]+variables[44]
rates[0] = variables[55]
variables[83] = variables[53]+variables[56]
variables[58] = variables[13]*variables[14]*log(variables[24]*states[2])
variables[84] = variables[58]
variables[82] = variables[37]*(exp(variables[83]/(variables[13]*variables[14]))-exp(variables[84]/(variables[13]*variables[14])))
variables[97] = variables[56]
variables[62] = variables[13]*variables[14]*log(variables[28]*states[4])
variables[98] = variables[62]
variables[96] = variables[42]*(exp(variables[97]/(variables[13]*variables[14]))-exp(variables[98]/(variables[13]*variables[14])))
variables[57] = variables[79]-variables[82]-variables[96]
rates[1] = variables[57]
variables[86] = variables[58]
variables[60] = variables[13]*variables[14]*log(variables[26]*states[3])
variables[87] = variables[60]
variables[85] = variables[38]*(exp(variables[86]/(variables[13]*variables[14]))-exp(variables[87]/(variables[13]*variables[14])))
variables[59] = variables[82]-variables[85]
rates[2] = variables[59]
variables[89] = variables[60]
variables[90] = variables[52]+variables[62]
variables[88] = variables[39]*(exp(variables[89]/(variables[13]*variables[14]))-exp(variables[90]/(variables[13]*variables[14])))
variables[61] = variables[85]-variables[88]
rates[3] = variables[61]
variables[92] = variables[62]
variables[93] = 2.0*variables[50]+variables[64]
variables[91] = variables[40]*(exp(variables[92]/(variables[13]*variables[14]))-exp(variables[93]/(variables[13]*variables[14])))
variables[63] = variables[88]-variables[91]+variables[96]
rates[4] = variables[63]
variables[65] = variables[91]-variables[44]
rates[5] = variables[65]
def compute_variables(voi, states, rates, variables):
variables[64] = variables[13]*variables[14]*log(variables[30]*states[5])
variables[94] = variables[64]-variables[73]
variables[54] = variables[13]*variables[14]*log(variables[20]*states[0])
variables[95] = variables[54]+variables[76]
variables[44] = variables[41]*(exp(variables[94]/(variables[13]*variables[14]))-exp(variables[95]/(variables[13]*variables[14])))
variables[43] = 2.0*variables[15]*-variables[44]
variables[80] = 2.0*variables[51]+variables[54]-variables[67]
variables[56] = variables[13]*variables[14]*log(variables[22]*states[1])
variables[81] = variables[56]+variables[70]
variables[79] = variables[36]*(exp(variables[80]/(variables[13]*variables[14]))-exp(variables[81]/(variables[13]*variables[14])))
variables[69] = variables[79]
variables[46] = variables[32]*variables[15]*variables[69]
variables[78] = variables[44]
variables[47] = variables[35]*variables[15]*variables[78]
variables[75] = variables[44]
variables[48] = variables[34]*variables[15]*variables[75]
variables[72] = variables[79]
variables[49] = variables[33]*variables[15]*variables[72]
variables[45] = variables[46]+variables[49]+variables[48]+variables[47]
variables[58] = variables[13]*variables[14]*log(variables[24]*states[2])
variables[60] = variables[13]*variables[14]*log(variables[26]*states[3])
variables[62] = variables[13]*variables[14]*log(variables[28]*states[4])
variables[83] = variables[53]+variables[56]
variables[84] = variables[58]
variables[82] = variables[37]*(exp(variables[83]/(variables[13]*variables[14]))-exp(variables[84]/(variables[13]*variables[14])))
variables[86] = variables[58]
variables[87] = variables[60]
variables[85] = variables[38]*(exp(variables[86]/(variables[13]*variables[14]))-exp(variables[87]/(variables[13]*variables[14])))
variables[89] = variables[60]
variables[90] = variables[52]+variables[62]
variables[88] = variables[39]*(exp(variables[89]/(variables[13]*variables[14]))-exp(variables[90]/(variables[13]*variables[14])))
variables[92] = variables[62]
variables[93] = 2.0*variables[50]+variables[64]
variables[91] = variables[40]*(exp(variables[92]/(variables[13]*variables[14]))-exp(variables[93]/(variables[13]*variables[14])))
variables[97] = variables[56]
variables[98] = variables[62]
variables[96] = variables[42]*(exp(variables[97]/(variables[13]*variables[14]))-exp(variables[98]/(variables[13]*variables[14])))
variables[55] = -variables[79]+variables[44]
variables[57] = variables[79]-variables[82]-variables[96]
variables[59] = variables[82]-variables[85]
variables[61] = variables[85]-variables[88]
variables[63] = variables[88]-variables[91]+variables[96]
variables[65] = variables[91]-variables[44]
